|
CSE 590C, Sp '11: Reading & Research in Comp. Bio. |
|
 CSE Home |
About Us |
Search |
Contact Info |
| Course Info |
CSE 590C is a weekly seminar on Readings and Research in
Computational Biology, open to all graduate students in computational,
biological, and mathematical sciences.
| |||||||||||||||||||||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||||||||||||||||||||||
| Schedule |
|
|||||||||||||||||||||||||||||||||||||||||||||||||
| Papers, etc. |
Links to full papers below are often to journals that require a
paid subscription. The UW Library is generally a paid
subscriber, and you can freely access these articles if you do
so from an on-campus computer. For off-campus access,
follow the "[offcampus]" links below or
look at the
library "proxy server" instructions.
You will be prompted for your UW net ID and password once per
session.
|
|||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract: Genomes are complex physical structures, and their dynamic
functional output-time dependent gene expression-is related to
spatial organization as well as local chromatin status. We seek to
define a general framework for mapping the dynamic relationship
between one-dimensional features, such as patterns of histone
modifications, transcription profiles and replication profiles, and
3D genome architecture constructed from integration of Hi-C (genome
conformation capture) and single cell interphase 3D-FISH
(fluorescent in situ hybridization). This dynamic relationship may
give insight into the process of cellular
differentiation. Typically, constructed biological networks exist in
an abstract space, where the positions of the network nodes are not
considered. We argue that geography matters greatly for network
function, and the nodes (genes) occupy particular positions in space
and reconfigure over time. To facilitate 3D analyses, we are
developing an automated computational tool for characterizing the
spatial architecture of the nucleus in a single cell. I will use an
example from our data to demonstrate this analysis.
Joint work with: Mark Groudine (FHCRC), David Scalzo (FHCRC), Michael Perlman (Statistics, UW), and John Snyder (Microsoft Research). Suggested reading:
|
05/02: Effective population size under the coalescent -- Julia Palacios, Statistics
05/09: -- The Fifth CMB Spring Symposium, 1:00-5:30, CSE 691
See link for details. The subsumes CSE 590C this week.
05/16: Open computational problems in microbiome research -- Sharon Greenblum & Roie Levy, Genome Sciences
05/23: Progress in Nimble Peptide Identification Software -- Benjamin Diament, CSE
05/30: -- Holiday
CSE's Computational Molecular Biology research group
Interdisciplinary Ph.D. program in Computational Molecular Biology
 |
Computer Science & Engineering University of Washington Box 352350 Seattle, WA 98195-2350 (206) 543-1695 voice, (206) 543-2969 FAX |
Note on Electronic Access to Journals